I just went through Boot Camp kicking its ass other than level 3-4 where I didn't get my perfect. I went back and replayed the level this time attaining the perfect rating, but the achievement didn't pop. Checked the stats and I was at 100%. So I played the 6th stage of that mission again (getting perfect, but I doubt it matters) and it popped. Because I played only the last stage and didn't get the requisite 3.5M points for the overall mission, it said I failed - but the achievement still popped.

So, it seems the game may only check for 100% Planet completion at the end of a mission. If you have to go back to get perfect on something else, you might need to replay the last stage to get it to unlock.